ukb_icd_freq_by {ukbtools}

Frequency of an ICD diagnosis by a target variable

Description

Produces either a dataframe of diagnosis frequencies or a plot. For a quantitative reference variable (e.g. BMI), the plot shows frequency of diagnosis within each group (deciles of the reference variable by default) at the (max - min) / 2 for each group.

Usage

ukb_icd_freq_by(data, reference.var, n.groups = 10,
  icd.code = c("^(I2[0-5])", "^(I6[0-9])",
  "^(J09|J1[0-9]|J2[0-2]|P23|U04)"),
  icd.labels = c("coronary artery disease", "cerebrovascular disease",
  "lower respiratory tract infection"), plot.title = "",
  legend.col = 1, legend.pos = "right", icd.version = 10,
  freq.plot = FALSE, reference.lab = "Reference variable",
  freq.lab = "UKB disease frequency")

Arguments

data

A UKB dataset (or subset) created with ukb_df.

reference.var

UKB ICD frequencies will be calculated by levels of this variable. If continuous, by default it is cut into 10 intervals of approximately equal size (set with n.groups).

n.groups

Number of approximately equal-sized groups to split a continuous variable into.

icd.code

ICD disease code(s) e.g. "I74". Use a regular expression to specify a broader set of diagnoses, e.g. "I" captures all Diseases of the circulatory system, I00-I99, "C|D[0-4]." captures all Neoplasms, C00-D49. Default is the WHO top 3 causes of death globally in 2015, see http://www.who.int/healthinfo/global_burden_disease/GlobalCOD_method_2000_2015.pdf?ua=1. Note. If you specify 'icd.codes', you must supply corresponding labels to 'icd.labels'.

icd.labels

Character vector of ICD labels for the plot legend. Default = V1 to VN.

plot.title

Title for the plot. Default describes the default icd.codes, WHO top 6 cause of death 2015.

legend.col

Number of columns for the legend. (Default = 1).

legend.pos

Legend position, default = "right".

icd.version

The ICD version (or revision) number, 9 or 10.

freq.plot

If TRUE returns a plot of ICD diagnosis by target variable. If FALSE (default) returns a dataframe.

reference.lab

An x-axis title for the reference variable.

freq.lab

A y-axis title for disease frequency.